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The order of sequence alignment can bias the selection of tree - mbe library arizona

The order of sequence alignment can bias the selection of tree - mbe library arizona 2025

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The document discusses how the order of sequence alignment can influence the selection of tree topology in phylogenetic analysis. It highlights that while differential substitution rates are known to bias tree assessments, the alignment order itself can also introduce significant biases. Using elongation factor Tu (EF-Tu) sequences, the author demonstrates that specific alignment orders favor certain tree topologies, suggesting that these order-dependent biases may be as important as unequal rate effects. The paper emphasizes the need for careful consideration of alignment methods to avoid misleading results in evolutionary studies.

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